<?xml version="1.0" encoding="us-ascii"?>
<!--XBRL document created with Toppan Merrill Bridge  9.6.8042.36810 -->
<!--Based on XBRL 2.1-->
<!--Created on: 3/11/2022 12:38:23 AM-->
<!--Modified on: 3/11/2022 12:38:23 AM-->
<xsd:schema targetNamespace="http://www.bioxceltherapeutics.com/20211231" attributeFormDefault="unqualified" elementFormDefault="qualified" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:btai="http://www.bioxceltherapeutics.com/20211231" xmlns:deprecated="http://www.xbrl.org/2009/role/deprecated" xmlns:currency="http://xbrl.sec.gov/currency/2021" xmlns:us-roles="http://fasb.org/us-roles/2021-01-31" xmlns:ref="http://www.xbrl.org/2006/ref" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" xmlns:xl="http://www.xbrl.org/2003/XLink" xmlns:us-types="http://fasb.org/us-types/2021-01-31" xmlns:srt-roles="http://fasb.org/srt-roles/2021-01-31" xmlns:utr="http://www.xbrl.org/2009/utr" xmlns:us-gaap="http://fasb.org/us-gaap/2021-01-31" xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:stpr="http://xbrl.sec.gov/stpr/2021" xmlns:sic="http://xbrl.sec.gov/sic/2021" xmlns:srt-types="http://fasb.org/srt-types/2021-01-31" xmlns:enum2="http://xbrl.org/2020/extensible-enumerations-2.0" xmlns:country="http://xbrl.sec.gov/country/2021" xmlns:net="http://www.xbrl.org/2009/role/net" xmlns:dei="http://xbrl.sec.gov/dei/2021q4" xmlns:naics="http://xbrl.sec.gov/naics/2021" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:dtr-types="http://www.xbrl.org/dtr/type/2020-01-21" xmlns:negated="http://www.xbrl.org/2009/role/negated" xmlns:exch="http://xbrl.sec.gov/exch/2021" xmlns:attributeFormDefault="unqualified" xmlns:srt="http://fasb.org/srt/2021-01-31" xmlns:xbrli="http://www.xbrl.org/2003/instance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <xsd:annotation>
    <xsd:appinfo>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/StatementBalanceSheets" id="StatementBalanceSheets">
        <link:definition>00100 - Statement - BALANCE SHEETS</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/StatementStatementsOfOperations" id="StatementStatementsOfOperations">
        <link:definition>00200 - Statement - STATEMENTS OF OPERATIONS</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/StatementStatementsOfCashFlows" id="StatementStatementsOfCashFlows">
        <link:definition>00400 - Statement - STATEMENTS OF CASH FLOWS</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosurePropertyAndEquipmentNetDetails" id="DisclosurePropertyAndEquipmentNetDetails">
        <link:definition>40701 - Disclosure - Property and Equipment, net (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureAccruedExpensesDetails" id="DisclosureAccruedExpensesDetails">
        <link:definition>40801 - Disclosure - Accrued Expenses (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureLeasesMaturitiesDetails" id="DisclosureLeasesMaturitiesDetails">
        <link:definition>41002 - Disclosure - Leases - Maturities (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureIncomeTaxesDeferredTaxDetails" id="DisclosureIncomeTaxesDeferredTaxDetails">
        <link:definition>41201 - Disclosure - Income Taxes - Deferred Tax (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureIncomeTaxesReconciliationDetails" id="DisclosureIncomeTaxesReconciliationDetails">
        <link:definition>41202 - Disclosure - Income Taxes - Reconciliation (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureLeasesMaturitiesOfOperatingLeaseLiabilityDetailsCalc2" id="DisclosureLeasesMaturitiesOfOperatingLeaseLiabilityDetailsCalc2">
        <link:definition>41202 - Disclosure - Leases - Maturities of Operating Lease Liability (Details) - Calc 2</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/StatementStatementsOfChangesInStockholdersEquity" id="StatementStatementsOfChangesInStockholdersEquity">
        <link:definition>00300 - Statement - STATEMENTS OF CHANGES IN STOCKHOLDERS' EQUITY</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/StatementStatementsOfChangesInStockholdersEquityParenthetical" id="StatementStatementsOfChangesInStockholdersEquityParenthetical">
        <link:definition>00305 - Statement - STATEMENTS OF CHANGES IN STOCKHOLDERS' EQUITY (Parenthetical)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureStockBasedCompensationTables" id="DisclosureStockBasedCompensationTables">
        <link:definition>30903 - Disclosure - Stock-Based Compensation (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureSummaryOfSignificantAccountingPoliciesDetails" id="DisclosureSummaryOfSignificantAccountingPoliciesDetails">
        <link:definition>40301 - Disclosure - Summary of Significant Accounting Policies (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureFinancingActivitiesDetails" id="DisclosureFinancingActivitiesDetails">
        <link:definition>40401 - Disclosure - Financing Activities (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureTransactionsWithBioxcelLlcDetails" id="DisclosureTransactionsWithBioxcelLlcDetails">
        <link:definition>40501 - Disclosure - Transactions with BioXcel LLC (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureStockBasedCompensationDescriptionDetails" id="DisclosureStockBasedCompensationDescriptionDetails">
        <link:definition>40901 - Disclosure - Stock-Based Compensation - Description (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureStockBasedCompensationStockOptionActivityDetails" id="DisclosureStockBasedCompensationStockOptionActivityDetails">
        <link:definition>40902 - Disclosure - Stock-Based Compensation - Stock Option Activity (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureStockBasedCompensationAssumptionsDetails" id="DisclosureStockBasedCompensationAssumptionsDetails">
        <link:definition>40903 - Disclosure - Stock-Based Compensation - Assumptions (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureStockBasedCompensationExpenseAndEsppDetails" id="DisclosureStockBasedCompensationExpenseAndEsppDetails">
        <link:definition>40904 - Disclosure - Stock-Based Compensation - Expense and ESPP (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DocumentDocumentAndEntityInformation" id="DocumentDocumentAndEntityInformation">
        <link:definition>00090 - Document - Document and Entity Information</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/StatementBalanceSheetsParenthetical" id="StatementBalanceSheetsParenthetical">
        <link:definition>00105 - Statement - BALANCE SHEETS (Parenthetical)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureNatureOfBusiness" id="DisclosureNatureOfBusiness">
        <link:definition>10101 - Disclosure - Nature of the Business</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureBasisOfPresentation" id="DisclosureBasisOfPresentation">
        <link:definition>10201 - Disclosure - Basis of Presentation</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureSummaryOfSignificantAccountingPolicies" id="DisclosureSummaryOfSignificantAccountingPolicies">
        <link:definition>10301 - Disclosure - Summary of Significant Accounting Policies</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureFinancingActivities" id="DisclosureFinancingActivities">
        <link:definition>10401 - Disclosure - Financing Activities</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureTransactionsWithBioxcelLlc" id="DisclosureTransactionsWithBioxcelLlc">
        <link:definition>10501 - Disclosure - Transactions with BioXcel LLC</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureEarningsLossPerShare" id="DisclosureEarningsLossPerShare">
        <link:definition>10601 - Disclosure - Earnings (Loss) Per Share</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosurePropertyAndEquipmentNet" id="DisclosurePropertyAndEquipmentNet">
        <link:definition>10701 - Disclosure - Property and Equipment, net</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureAccruedExpenses" id="DisclosureAccruedExpenses">
        <link:definition>10801 - Disclosure - Accrued Expenses</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureStockBasedCompensation" id="DisclosureStockBasedCompensation">
        <link:definition>10901 - Disclosure - Stock-Based Compensation</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureLeases" id="DisclosureLeases">
        <link:definition>11001 - Disclosure - Leases</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureCommitmentsAndContingencies" id="DisclosureCommitmentsAndContingencies">
        <link:definition>11101 - Disclosure - Commitments and Contingencies</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureIncomeTaxes" id="DisclosureIncomeTaxes">
        <link:definition>11201 - Disclosure - Income Taxes</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureSummaryOfSignificantAccountingPoliciesPolicies" id="DisclosureSummaryOfSignificantAccountingPoliciesPolicies">
        <link:definition>20302 - Disclosure - Summary of Significant Accounting Policies (Policies)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureSummaryOfSignificantAccountingPoliciesTables" id="DisclosureSummaryOfSignificantAccountingPoliciesTables">
        <link:definition>30303 - Disclosure - Summary of Significant Accounting Policies (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureTransactionsWithBioxcelLlcTables" id="DisclosureTransactionsWithBioxcelLlcTables">
        <link:definition>30503 - Disclosure - Transactions with BioXcel LLC (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureEarningsLossPerShareTables" id="DisclosureEarningsLossPerShareTables">
        <link:definition>30603 - Disclosure - Earnings (Loss) Per Share (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosurePropertyAndEquipmentNetTables" id="DisclosurePropertyAndEquipmentNetTables">
        <link:definition>30703 - Disclosure - Property and Equipment, net (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureAccruedExpensesTables" id="DisclosureAccruedExpensesTables">
        <link:definition>30803 - Disclosure - Accrued Expenses (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureLeasesTables" id="DisclosureLeasesTables">
        <link:definition>31003 - Disclosure - Leases (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureIncomeTaxesTables" id="DisclosureIncomeTaxesTables">
        <link:definition>31203 - Disclosure - Income Taxes (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureNatureOfBusinessDetails" id="DisclosureNatureOfBusinessDetails">
        <link:definition>40101 - Disclosure - Nature of the Business (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureEarningsLossPerShareDetails" id="DisclosureEarningsLossPerShareDetails">
        <link:definition>40601 - Disclosure - Earnings (Loss) Per Share (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureLeasesDetails" id="DisclosureLeasesDetails">
        <link:definition>41001 - Disclosure - Leases (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureLeasesAdditionalInformationDetails" id="DisclosureLeasesAdditionalInformationDetails">
        <link:definition>41003 - Disclosure - Leases - Additional Information (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:linkbaseRef xlink:type="simple" xlink:href="btai-20211231_pre.xml" xlink:role="http://www.xbrl.org/2003/role/presentationLinkbaseRef" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" />
      <link:linkbaseRef xlink:type="simple" xlink:href="btai-20211231_cal.xml" xlink:title="Calculation Links, all" xlink:role="http://www.xbrl.org/2003/role/calculationLinkbaseRef" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" />
      <link:linkbaseRef xlink:type="simple" xlink:href="btai-20211231_def.xml" xlink:role="http://www.xbrl.org/2003/role/definitionLinkbaseRef" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" />
      <link:linkbaseRef xlink:type="simple" xlink:href="btai-20211231_lab.xml" xlink:role="http://www.xbrl.org/2003/role/labelLinkbaseRef" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" />
      <link:roleType roleURI="http://www.bioxceltherapeutics.com/role/DisclosureStandardAndCustomAxisDomainDefaults" id="DisclosureStandardAndCustomAxisDomainDefaults">
        <link:definition>99900 - Disclosure - Standard And Custom Axis Domain Defaults</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
    </xsd:appinfo>
  </xsd:annotation>
  <xsd:import namespace="http://xbrl.sec.gov/dei/2021q4" schemaLocation="https://xbrl.sec.gov/dei/2021q4/dei-2021q4.xsd" />
  <xsd:import namespace="http://www.xbrl.org/2009/role/negated" schemaLocation="http://www.xbrl.org/lrr/role/negated-2009-12-16.xsd" />
  <xsd:import namespace="http://www.xbrl.org/dtr/type/2020-01-21" schemaLocation="https://www.xbrl.org/dtr/type/2020-01-21/types.xsd" />
  <xsd:import namespace="http://www.xbrl.org/2003/instance" schemaLocation="http://www.xbrl.org/2003/xbrl-instance-2003-12-31.xsd" />
  <xsd:import namespace="http://xbrl.org/2005/xbrldt" schemaLocation="http://www.xbrl.org/2005/xbrldt-2005.xsd" />
  <xsd:import namespace="http://fasb.org/us-roles/2021-01-31" schemaLocation="https://xbrl.fasb.org/us-gaap/2021/elts/us-roles-2021-01-31.xsd" />
  <xsd:import namespace="http://fasb.org/us-gaap/2021-01-31" schemaLocation="https://xbrl.fasb.org/us-gaap/2021/elts/us-gaap-2021-01-31.xsd" />
  <xsd:import namespace="http://fasb.org/srt/2021-01-31" schemaLocation="https://xbrl.fasb.org/srt/2021/elts/srt-2021-01-31.xsd" />
  <xsd:element name="OrganizationAndPrincipalActivitiesAbstract" id="btai_OrganizationAndPrincipalActivitiesAbstract" type="xbrli:stringItemType" substitutionGroup="xbrli:item" abstract="true" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="NumberOfAdvancedProgram" id="btai_NumberOfAdvancedProgram" type="xbrli:integerItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="DevelopmentMilestonesMember" id="btai_DevelopmentMilestonesMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" abstract="true" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="SalesMilestonesMember" id="btai_SalesMilestonesMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" abstract="true" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="CollaborativeArrangementMilestonePaymentsPotential" id="btai_CollaborativeArrangementMilestonePaymentsPotential" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:balance="credit" xbrli:periodType="instant" />
  <xsd:element name="BioxcelCorporationMember" id="btai_BioxcelCorporationMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" abstract="true" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="LesseeOperatingLeaseNumberOfRenewal" id="btai_LesseeOperatingLeaseNumberOfRenewal" type="xbrli:integerItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="LesseeOperatingLeaseRenewalAtPercentageOfMarketRates" id="btai_LesseeOperatingLeaseRenewalAtPercentageOfMarketRates" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="CollaborativeArrangementMilestonePotentialPercent" id="btai_CollaborativeArrangementMilestonePotentialPercent" type="xbrli:pureItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="instant" />
  <xsd:element name="PatentCostsPolicyTextBlock" id="btai_PatentCostsPolicyTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="JefferiesMember" id="btai_JefferiesMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" abstract="true" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="ExpensesAccruedUnderContractualArrangementsWithClinicalResearchOrganizationsPolicyPolicyTextBlock" id="btai_ExpensesAccruedUnderContractualArrangementsWithClinicalResearchOrganizationsPolicyPolicyTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="IncentiveAwardPlan2020Member" id="btai_IncentiveAwardPlan2020Member" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" abstract="true" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="ShareBasedCompensationArrangementByShareBasedPaymentAwardPercentageOfIncreaseInCommonStockAvailableForGrant" id="btai_ShareBasedCompensationArrangementByShareBasedPaymentAwardPercentageOfIncreaseInCommonStockAvailableForGrant" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="EmployeeStockPurchasePlan2020Member" id="btai_EmployeeStockPurchasePlan2020Member" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" abstract="true" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="EmployeeStockPurchasePlanMaximumNumberOfSharesIssuedOrTransferred" id="btai_EmployeeStockPurchasePlanMaximumNumberOfSharesIssuedOrTransferred" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="StockPlan2017Member" id="btai_StockPlan2017Member" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" abstract="true" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="AccruedResearchAndDevelopmentExpenses" id="btai_AccruedResearchAndDevelopmentExpenses" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:balance="credit" xbrli:periodType="instant" />
  <xsd:element name="UnderwritersOptionExercisablePeriod" id="btai_UnderwritersOptionExercisablePeriod" type="xbrli:durationItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="AreaOfAdditionSpaceLeased" id="btai_AreaOfAdditionSpaceLeased" type="dtr-types:areaItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="NumberOfSharesAvailableForPurchase" id="btai_NumberOfSharesAvailableForPurchase" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="FinancingActivitiesAbstract" id="btai_FinancingActivitiesAbstract" type="xbrli:stringItemType" substitutionGroup="xbrli:item" abstract="true" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="FinancingActivitiesDisclosureTextBlock" id="btai_FinancingActivitiesDisclosureTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsCancelledInPeriod" id="btai_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsCancelledInPeriod" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsCancelledInPeriodWeightedAverageExercisePrice" id="btai_ShareBasedCompensationArrangementsByShareBasedPaymentAwardOptionsCancelledInPeriodWeightedAverageExercisePrice" type="dtr-types:perShareItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="ScheduleOfPropertyPlantAndEquipmentUsefulLivesTableTextBlock" id="btai_ScheduleOfPropertyPlantAndEquipmentUsefulLivesTableTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:periodType="duration" />
  <xsd:element name="DeferredTaxAssetsLeaseAccountingLiability" id="btai_DeferredTaxAssetsLeaseAccountingLiability" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:balance="debit" xbrli:periodType="instant" />
  <xsd:element name="DeferredTaxAssetsCapitalizedResearchAndDevelopment" id="btai_DeferredTaxAssetsCapitalizedResearchAndDevelopment" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:balance="debit" xbrli:periodType="instant" />
  <xsd:element name="OperatingLossCarryforwardsNoExpiration" id="btai_OperatingLossCarryforwardsNoExpiration" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:balance="debit" xbrli:periodType="instant" />
  <xsd:element name="IncreaseDecreaseInOperatingLeaseRightOfUseAssets" id="btai_IncreaseDecreaseInOperatingLeaseRightOfUseAssets" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" nillable="true" xbrli:balance="credit" xbrli:periodType="duration" />
  <xsd:element name="DeferredTaxAssetsUnrealizedGain" id="btai_DeferredTaxAssetsUnrealizedGain" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" abstract="false" nillable="true" xbrli:balance="debit" xbrli:periodType="instant" />
  <xsd:element name="RegisteredOfferingMember" id="btai_RegisteredOfferingMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" abstract="true" nillable="true" xbrli:periodType="duration" />
</xsd:schema>
